Plot

Pokémon XD: Gale of Darkness starts out by showing a cut scene of a boat caught in a storm at sea. This boat is then attacked by an evil looking Pokémon (Lugia). Now you control Michael in a one-on-one battle with your Salamence against a Metagross. After you win, you find out it was just a battle simulator in the Pokémon HQ Lab, a Pokémon lab your mother works at. Then your mom Lily gives you your P*DA and asks you to go find your sister Jovi. You go to an ominous and spooky house with a statue of Groudon in a fountain called Kaminko's house. When you get to the front door, you get stopped by Kaminko's assistant, Chobin, who thinks your a burglar and challenges you to a battle (this is a very common theme throughout the game). After you beat him, you get Jovi and return to the lab. As a reward, Professor Krane, the head scientist at the lab, gives you your very own Snag Machine, which can steal Shadow Pokémon from opposing trainers so you can purify them.

Soon after, Krane gets ambushed by a few members of Cipher. You have to battle one of them, known as Naps, whom holds the game's first Shadow Pokémon a Teddiursa. After you beat him, Cipher takes Krane and drives away. Lily, knowing that the purification chamber must be completed, asks you to go to Gateon Port to get a machine part for the chamber. When you arrive, Jovi runs into a thug named Zook. Just when things look ugly and he's about to attack you with a Shadow Zangoose, a weird man named Verich comes and interferes. One of his right-hand men, Ardos, destroys the Zangoose with his Alakazam in one hit. Soon after, you can choose to evolve your Eevee with any of the stones. In addition, you get the machine part you wanted from a young man named Perr and you meet his father Makan at Kaminko's Manor after fighting Chobin again who thinks you are a burglar again. After giving it to Lily, she asks you to go to Agate Village. At Agate Village, you meet Eagun and find the Relic Stone which Eagun lets you use after you defeat several trainers and himself, a mystical stone that can purify Shadow Pokémon. After, Eagun tells you to go to Mt. Battle and ask a man named Vander about Cipher. After helping Vander he tells you to inspect an old Cipher facility in the south that might have activity. When you get to the facility, you defeat everyone there including the Hexagon Brothers, Naps, the admin, Lovrina, all the while snagging Shadow Pokémon. You rescue Krane and return him to the lab. Then, an assistant tells you to go to Pyrite Town and deliver a disk to Nett (and meet Bitt and Secc) that may contain information about Cipher. When you arrive at your location you witness a cop telling two guys by the name of Trudly and Folly to stay out of town. Nett tells you it will take time to decipher it so he sends you off to a Rock Poke Spot to meet Duking and when you help Duking by demonstrating how to lure Pokémon in an interview Duking gives you the location of the Oasis Poké Spot which when you visit He gives you the location of the last Cave Poké Spot where you run into Trudly and Folly and meet and battle Wanderer Miror B. and snag his Shadow Voltorb before they run off accidentally leaving a device that tracks Miror B. so you can find him whenever. When you come back to Pyrite, you'll see that the building will be taken over by Cipher. After you defeat everyone including Cipher Commander Exol (the big buff guy) who helped kidnap Professor Krane and you also Snag their Shadow Pokémon, after the Cipher agents wipe the Databanks and leave Nett will tell you that on the disk it said that Cipher will attack Phenac City.

When you first enter Phenac City, a woman will stop you, tell you that you're the 1,000,000th visitor, give you some battle CDs, and send you off to Realgem Tower. You find Trudly and Folly blabbing on about the Battle CDs. They feel like throwing them in places all around Orre. You can explore Realgam Tower's Battle Bingo, Battle Sims, and Colosseum (not up and running yet).

Then head back to Phenac City. You head over to the Mayor's House. The secretary won't let you upstairs into the Mayor's room, so you'll have to find a distraction. She says she'd like some music so... take the CD you found back to the Mayor's House. Give then give it to the secretary. She plays the music, leaving the entrance to upstairs wide open. The Mayor isn't upstairs, but there is a note on the bed. It's a note from the Mayor to Justy, telling Justy of Cipher's plan. The note appears to have been cut short. The secretary then comes up and reveals herself as a Cipher Peon and after you defeat her and her back-up they retreat.

Head outside, and you'll see Justy walk out of the Pre Gym... six times. It's the Hexagon Brothers in disguise. Track down all six of them and the other imposters around town. After they're dealt with and you've snagged their Shadow Pokémon, Fostin will spill the beans. Almost all of the townsfolk that have been impersonated are in the Pre Gym's basement. You'll need the Elevator Key, which nether Fostin nor anyone else so far has... Head outside and talk to the little boy. There's commotion up in Phenac Stadium, at the farthest north in the city.

After Michael fights his way through the few remaining present Cipher Peons he challenges the Cipher Admin Snattle who reveals he will be the governor of Orre if the Cipher plan works. After Michael destroys Snattle in a Pokémon battle, he'll will run off and the news reporter and cameraman who were hostage tell you they got the whole confrontation on tape. Pick up what Snattle dropped when he fleed. It's the Elevator Key. Head to the Pre-Gym, use the Elevator Key on the elevator, and you can free the innocent citizens. Justy will ask for your P*DA number. Give it to him, and he'll give you a hint that there's a few shady characters going somewhere in the desert.

When you try to get to the ship that was attacked by Shadow Lugia (the evil looking Pokémon) you won't be able to because there is too much sand and your scooters tires get stuck. The head of ONBS will call you into his office to help find a little girl's Bonsly. After you promise to find the Pokémon Nett notices you are covered in sand and after hearing your story his friend Bitt suggests Perr to find a solution to your problem. When you go to Gaten Port Perr can't handle equipment of the likes you need yet so he asks you to go get his dad. You go to the Kaminko's Manor and after fighting Chobin and Chobin in a Pokémon battle suit called Robo Groundon Chobin you are given access to the Manor where you discuss with Makan your problem and after he promises to help you, you go back to Gaten Port so he can upgrade your scooter. Then you can be able to get to the ship.

When you reach the ship and start exploring it by going through a hole in the hull you run into three Cipher agents on the deck, one of them is Cipher Admin Gorigan who orders his men to deal with you as he heads back to his lair but one of the Peons makes an excuse to dump the responsibility of battling you on his comrade who is defeated. After the last Cipher Agent runs off a strange man comes out of the wheelhouse and explains that he has made the wrecked ship his home and that you can rest at his place in the wheelhouse and asks you to search the ship as strange sounds are coming from the storage. As Michael makes his way through the ship using boxes to make bridges and clear routes he eventually finds out that the source of the sounds is the little girls' Bonsly that he promised to find and when he almost sneaks up on it your P*DA rings and startles the Bonsly out of the ship and when you report this to the ships inhabitant the man is relieved the sounds were just a Pokémon and says it will probably head for somewhere more suited for Pokémon which causes Michael to immediately guess that the Bonsly will head for a Poké Spot. As you leave the ship a bunch of Team Snagem grunts show up led by Wakim their second-in-command, who uses his Pokémon Gloom to knock you out with Sleep powder and takes your snag machine.

When you wake up in the ship the ship man asks you why the grunts attacked you and when you explain what has been happening the ship man points you in the direction that the grunts went and you follow them to the Cipher Key Lair where you witness Zook destroy Wakim in a Pokémon battle after which Wakim and his men flee. You then battle Zook and beat him though you can't snag his Shadow Zangoose right now. When you leave the Lair you get an email from Secc who asks you to come to Pyrite Town where after you explain how you lost your Snag Machine. Secc will then directs you to the Outskirt Stand where a man has information for you, when you get there you run into Miror B. and battle and defeat his team including a Shadow Nosepass which you can't snag now. When they flee and you go inside a man named Hordel who used to work for Cipher escaped with a Shadow Togepi which he gives to you after telling you that the Cipher Key Lair is a factory for creating Shadow Pokémon. Secc then emails you the location of Team Snagem's Base where you fight through the Snagem Thugs and eventually battle GonzapSnagem's Head Leader for your Snag Machine after which he lets you walk out.
When you return to the Cipher Key Lair You defeat Zook again this time snagging his Zangoose and after that Zook quits and Gonzap and Wakim show up and deal with the other two guards allowing you to get inside the Lair where you battle and snag your way to the Cipher Admin Gorigan who after the battle threatens to blow up the factory. He is stopped by Verich who appears on the TV screen and reveals himself to be Grand Master Greevil of Cipher and that the XD001 has been perfected to withstand purification, he also tells you his base is on Citadark Isle. The TV then turns off, and Gorigan flees. You then pick up a full list of the Shadow Pokémon and when you are going back to the entrance you hear that Miror B. and his goons stole a Shadow Dragonitefrom Cipher.
You head to Gateon Port Where Makan reveals that the Robo Kyogre is finished and will take you to Citadark Isle. You should go back to the Pokémon HQ Lab to receive the Master Ball from Professor Krane. You then go to Citadark Isle and fight and snag your way through a lot of Cipher agents and Admins including Greevils Bodyguards and sons (Ardos & Eldes) until you reach Greevil who's plan is to have an army of Shadow Pokémon he then orders the Shadow Lugia to attack you at which you simply catch it immediately with the Master Ball. Greevil will then battle you with his team of all Shadow Pokémon including Rhydon, Moltres, Exeggutor, Tauros, Articuno, and Zapdos at which you catch all of them.

Greevil is crushed and dejected as Ardos comes into the room. He recommends destroying the whole island with you still on it. Greevil, however, says that it would destroy the shadow Pokémon data and all his allies as well, so it's not a great idea. Ardos, however, argues that those things can be replaced. He has a helicopter ready for their escape, but Eldes shows up, and is ashamed of Ardos. He's a lot more moral and honorable. Ardos says that clinging to honor will be the end of Cipher and that's no good. Greevil reluctantly agrees. Eldes says that Cipher is already finished, and there's no point in escaping, because they have to start from scratch anyways. Ardos is still stubborn, and orders Greevil to destroy the island. Greevil apologises for being about to destroy the island, but Eldes, Greevil's son, urges him once more, to stop. Eldes says that Greevil can't take over the world with just strong Pokémon, and points to you as an example. Ardos tries to quiet Eldes down, but he won't have any of it. Eldes offers his hand to Greevil to stand again and regain some dignity. Eldes then takes you aside and thanks you for ending this nightmare. He looks forward to battling you in the future, but not as enemies. Suddenly, the storm around Citadark Isle breaks and when you arrive back there is a huge celebration in your honor. Even Jovi is happy to have you home. The game saves, and finishes. But is that the end? Nope. You wake up in your Bedroom at the Pokémon HQ Lab and go outside and battle Eugun and then you can purify the Lugia with the go and catch the last Shadow Pokémon from Miror B. After you snag his Dragonite and defeat him he destroys the device that tracks him. Oh well you've got the last Shadow Pokémon.